Chaos and Discord: Infection
by King Xeno
Summary: Tails had to help, he just had to. His best friend had been taken over by some virus and it was up to him to save them all! With the help of friends, old and new, he may just be able to do it. All of Equestria was counting on him. The third part of the Chaos and Discord series! No OCs accepted for this one, a few have already been chosen.
1. Prologue

Prologue: Spreading Infection

The Manticore chased the rabbit through the large cave, the Manticore couldn't quite reach the rabbit, who had an advantage in speed. However it seemed the cave moved on forever, until they came across a cavern, where there was a single spring, there were three dead bodies lying there, which seemed to captivate the Manticore, a meal that wouldn't run. It began to feast while the rabbit attempted to drink from the nearby spring. The rabbit lost its balance and fell into the spring, bubble were floating to the surface, but the Manticore was still hungry. It sat waiting for the rabbit to surface, but instead a large clawed hand reached out, flesh was falling off and you could see the bloody bone underneath. The hand grasped at the Manticore who began backing up. The rabbit surfaced, it was falling apart, an eye fell from the socket into the spring, and it crawled, now that it has lost its hind legs. The rabbit let out a loud moan of anger, and attempted to claw the Manticore, but it fled, while the rabbit moved past, looking for something to satisfy its hunger.

The rabbit found something, it was a hedgehog, he was blue and strange, but the rabbit had the element of surprise. It leapt at the hedgehog and bit his right arm, while the hedgehog flung the rabbit away. The rabbit, knew what that bite would do, and the results would be destructive, it began to move on searching for something another to attack, only be get caught in a cage while a tan earth pony stood near the cage. "What the…?"


	2. Chapter 1

Hey guys! It is to my knowledge that Sonic has a brother, he is Tails, but not blood related, more of a taking in sort of thing. So I'm sticking by that! I'm going to be making the chapters a little lengthier (About 5,000 words, including chapter name, and author notes) so I can get a bit more in each chapter, but the chapters will be the same amount. The reason I'm telling you this is so you don't worry about the updates taking forever. Trust me I am not going to abandon this story!

Chapter 1: Turning Point (Meeting Others)

Twilight and Fluttershy looked at the creature before them, while it resembled a rabbit, it seemed to be a moving decaying corpse. The "rabbit" had large claws on the end of its paws, while it had grown razor sharp fangs, its eyes had taken on a reptilian appearance, and finally it was literally falling apart. "Gizmo, how did you find this creature?" Twilight asked, looking at the tan earth pony, he moved his curly blonde mane out of his emerald green eyes and smiled. "I was testing out a new invention. A cage that you can hide under leaves or dirt, and it has this pressure plate. When something steps on it… BAM! The cage traps it! I was going to let the little guy go until I saw him like this." He explained motioning towards the cage with his hoof.

"He seems to not be in any pain, but those fangs are producing some form of toxin, not deadly, but who knows what could happen." Twilight muttered, while quickly scribbling down some notes. She looked at the rabbit and sighed. "We can't do much about it right now, we'd need someone with extreme intelligence! Someone who can really be of use! We need…!" She had begun but a loud crash outside the library broke her away from her sentence. Sonic looked up from his book, and got onto his feet. "I'll check it out." He said, which let Twilight get a good look at his arm. She saw the red bite marks and stopped him. "Sonic, what is that?" She asked, he tensed up and said "A bite mark…" "How did you get it?" She asked narrowing her eyes. "I may or may not have been taking a late night run through the Everfree forest…" Sonic replied, waiting for her to shout. "Just be more careful next time." She said with a sigh.

Sonic walked outside and began looking for what might have caused the sound, when he heard an all too familiar voice. "HELP! I'M STUCK!" Sonic scanned the area searching for the source of the muffled voice. He saw someone with their head stuck in the ground. He smiled and began to dig out the yellow fox. "Tails! How did you get here?" Sonic asked, once he had gotten out of the hole. "Sonic? Wait… Does this mean…? I'm in…?" Tails had begun to sound worried. "Hey calm down! The ponies here are friendly, you don't need to worry." Sonic said, making his brother let out a sigh of relief. "So, how have things been back in Station Square?" Sonic asked, while they walked back towards the library. "Things have been peaceful, a little too peaceful, you know?" Tails replied. They entered the library and Fluttershy let out a startled shriek.

"Fluttershy! Are you ok?" Gizmo asked, helping her onto her hooves. "Yes… I just wasn't expecting Sonic to bring anyone back." She replied, attempting to catch her breath. "Sonic, who is this?" Twilight asked, looking at the yellow fox with two tails. Sonic smiled and replied "This? He's my little brother! Twilight I'd like for you to meet Tails." Sonic said, pushing the yellow fox forward. "You're Tails? Sonic's told us so much about you!" Twilight happily chattered. "You must be Twilight. Sonic's girlfriend right?" Tails asked. "A lot more now buddy, we're parents." Sonic replied. "You are!? Well I guess it has been years since we'd last spoken." Tails replied, rubbing the back of his head. "Well, we could use your help. We've got this animal, and we aren't sure of why it's in this condition…" Twilight began to explain, but Tails nodded and began to inspect the creature. He revealed a syringe and stuck it into the animals hide, extracting a small amount of blood.

He pulled out a device about as big as his hand and inserted the needle into one end. After a few seconds it began to dispense a long strip of paper. He pulled it out straight and began to read what it said. "Genus Sylvilagus, or commonly known as a Cottontail Rabbit. Subject seems to have gone through heavy mutation… Cause is undeterminable…" He spoke out the words carefully and calmly. "A cottontail rabbit?" Fluttershy asked, looking the cage. It growled at her before letting out a loud screech. "Whoa! Sounds like the little guy is seriously pissed off!" Gizmo said, staring at the small animal. Fluttershy looked at the rabbit and began to move closer to him. "I'm sure all he needs is a little love and affec… OW!" Fluttershy shouted, the rabbit had its teeth embedded in her flesh, she stared as the rabbit refused to let go. Sonic grabbed a book and began to beat the small animal on the head, until it let go.

Fluttershy looked at the bleeding bite mark, and Sonic gasped. He moved his arm close to her leg, his scars matched the fresh bite exactly. "Oh… My… God…" Sonic muttered looking up. Twilight was shocked, this thing had bitten Sonic as well. "So it's bitten you too?" Gizmo asked, before asking "How many more has it bitten?" Twilight began to speak quickly and rapidly "We have to find out if anypony else has been bitten. We'll split up, Sonic and Fluttershy… You two stay here… I'll go get Speedy and Spike." Sonic nodded, while Twilight rushed upstairs.

* * *

><p>Sonic, Fluttershy, Derpy, Silver, Scourge, Trixie, and Applebloom, were escorted into a hidden location, personally by Princesses Luna, Celestia and Cadence. They entered the stone building, heavily guarded, with a medical staff on standby to record and results. "We're sorry, but until we can determine the effects of this creature's poison, you all must remain here. Once we have it all sorted out, we will release you." Celestia said with a frown. "We understand Princess. It's for the greater good." Sonic replied. "Sonic, I'm trusting you keep them all under control." She added, Sonic replied with a nod and the three Princesses left.<p>

"Well this is just great isn't it?" Scourge asked. "We get bitten by a rabbit and we're locked up like some kind of monster?" Scourge finished while Sonic let out an annoyed sigh. He led the others to a large room with several beds, before sitting on one. "Might as well get comfortable…" Sonic muttered. He heard someone groan in pain, looking over it was Fluttershy, she had one leg over her stomach, and her face was frozen in pure agony. She fell over, and Sonic jumped up. "Fluttershy! Are you ok?" He asked, forcing open one of her eyes, it was beginning to shake, he saw her pupils change shape, moving to a lizard like slit. She groaned as her teeth began to grow creating four large fangs that prevented her from closing her mouth. Sonic had a tight hold on her face, as a result a chunk of flesh was accidentally ripped away with ease. Fluttershy let out a hiss that sounded like it came straight from a sci-fi movie. She lunged at him sinking her teeth into his neck, injecting more of the poison into his veins. He attempted to force her off, but found he couldn't.

Scourge grabbed her by the neck and yanked her off, he put her in a head lock, she struggled for breath against his grip, but eventually she went limp. "Scourge! Did you kill her?" Silver asked, running forward. "No, I cut off oxygen until she passed out." Scourge replied, as doctors and scientists rushed into the room, and began bandaging Sonic's neck. Several guards lifted the unconscious Fluttershy and took out of the room, leaving everyone there in silence. "Will that happen to us?" Applebloom asked, she was obviously frightened and she had a reason to be so. "I think it will." Silver replied before the group fell into an eerie silence.

* * *

><p>Sonic sat in the room, he was alone. All the others had turned, Scourge, Silver, Trixie, Derpy, and even sweet little Applebloom. He knew he would be next, it's only logical, but nothing could save him from his fate.<p>

Sonic sat with his knees against his chest, his arms resting on them, he stared straight ahead of him. He was crying but his tears had dried up hours ago. He felt a sharp pain in his chest, he knew that it would happen soon so he was prepared, but he would never be prepared for the result. The pain intensified, making him yell in pure agony, he began to grab at his chest, until he felt the change begin. He noticed the large mirror next to him and saw the horrors unfold. His gloves began to tear, revealing bone from the decaying flesh. He saw his teeth grow, when he tried to close his mouth the four fangs hit each other, making it impossible. He finally saw his eyes begin to change, which would be the last sign. There was a wet smacking sound as chunk of his skin and muscle hit the stone floors. He grabbed at his face, his left eye fell out of its socket. Sonic let out a loud roar, a signal that the transformation was complete. He felt strange like he couldn't think properly. Several armed guards entered the room, and Sonic charged at the nearest one.

He bit down on one guard, who let out a cry of pain, while the others attempted to free him from Sonic's grip. He let out a loud hiss and jumped from guard to guard until they were all bitten. He managed to avoid them and rushed into the facility, scaring scientists and doctors as he ran past. He began to slam all of his body weight into a metal door, and eventually broke it down. He saw the others, all trapped inside strange cylinders filled with a blue liquid. "Subject S-1 has escaped! Requesting immediate lock down!" A scientist shouted. Sonic approached him slowly, taking time with each step. The pony backed up until he hit one of the tubes, knocking it over, creating a domino effect. The tubes shattered releasing the others, who turned to face the scientist. "No! No! NOOOOOOOOOOOOOOOO...!" Sonic turned to face his infected brethren, each one had begun to decay, chunks of flesh having been removed. They ran out the room, leaving the scientist, who was gasping for breath. "GODDAMMIT! I PISSED MY FUCKING PANTS!" He shouted, after a few moments.

The seven of them ran down the halls attacking anything in their path, guards, scientists, and doctors. They were heading towards the main point of research, where they were attempting to develop a cure. Guards were falling left and right, but the room had many guards inside. "Don't kill them! We have to capture them!" A scientist shouted. "Why? Those things are monsters!" A guard asked. "One of those 'Monsters' is royalty!" The scientist replied. Sonic led Silver and Fluttershy down a left hall, while Scourge led Derpy, Trixie, and Applebloom down the right. Both doors would be vulnerable, but the left was quickly shut, preventing any form of entrance. "One two three... AH! THEY'VE SPLIT UP!" A guard shouted rushing to the other door. Scourge was approaching his door, and the guard was just as close, but the guard managed to shut the door, preventing Scourge from entering. "Mother fuckers, they've drilled us in here!" The guard shouted leaning on the door.

"You need to calm down!" "How can I? We have a fucking zombie apocalypse going on!" Sonic watched the guards argue, he began to slam into the door, while the others did the same. The doors began to dent from the onslaught, but they did not break. Sonic began to wonder how they would get in, after all a cure could not be created. His mind was clearing he was starting to regain some of his senses as the poison finally settled. Sonic grabbed onto the handle of the door and stumbled in, almost in a drunk like fashion. He looked up at the guards and asked "What? You never seen a hedgehog before?" The guards rushed forward while the others began to come around as well. "What… Happened…?" Sonic asked, while a guard moved over to assist him. When the guard was in range, Sonic bit down on his neck, injecting the poison in him. "You really should have just killed us…" Sonic muttered before leaping forward with his fangs ready.

* * *

><p>Sonic watched as the guards and scientists slowly turned one by one, until the entire facility was under their control. "They will be in an animal like state, at least for a few minutes… After all we came through didn't we?" Sonic asked, looking at the others. "So strange… Being alive and dead… At the same time…" Scourge muttered. Sonic laughed and said "You think we're dead? Not at all, this is simply a virus… Planned to spread… After all this virus has some advantages doesn't it?" Sonic asked. They nodded while Sonic let out a laugh. "I mean this is amazing… New powers we had never had." Silver said, pulling a spear out of his torso. "This must be spread, it must be shared with all life! It must be known throughout all of Equestria!" Sonic shouted, watching the newly infected rise. A single non infected pony rose up, he had been unconscious and saw Sonic standing over him. "You are lucky." Sonic said with a smile. "What do you mean?" The pony asked, backing slowly away from the blue hedgehog. "You are the only one who will not become one of us. If you do me one favor… Run… Run to your little Princesses and tell them the Infected come!" Sonic shouted, while the pony got onto his hooves and bolted in the opposite direction.<p>

* * *

><p>Tails looked at the rabbit, it had begun to act like a rabbit again, but only when it was hungry or thirsty. Otherwise he wasn't able to approach it, making research difficult. "Uncle Tails?" Speedy asked, getting the fox's attention. Tails looked at his niece and smiled. "What can I do for you?" Tails asked, while Speedy nervously tapped her hooves on the ground. "Mom wanted me to tell you that lunch is ready." She said, not depressed, but not happy, more emotionless, like a robot. Tails frowned as Speedy walked away. "It's gotta be hard on her, not to mention Twilight, and then there's Rarity… Not to mention Applejack…" Tails muttered, he cleaned of his tools and moved into the kitchen, where Twilight and Spike had made lunch. "Thanks Twilight. Thanks Spike." Tail said sitting at a table, he then began to nibble at a sandwich while writing down some notes.<p>

"You know Tails, you should really take a break. See some of your other friends. I'm sure they'd be glad to know you're here." Spike said, watching Tails scribble on the notepad. "Spike is right, you need a bit of fresh air. I'll take you around town." Twilight offered, but Tails didn't reply, he continued to write. Spike walked past and stepped on something, making a loud crack ring through the tree. Tails looked and saw he had snapped the thick metal of a syringe, it had been standing point up. "Sorry Tails! I didn't see that there!" Spike said picking up the metal. "Why didn't that hurt you?" Tails asked looking at Spike curiously. "I'm a dragon! I've got tough scales! Lava doesn't even hurt me!" Spike boasted crossing his arms in a triumphant matter. Tails shot up and shouted "OF COURSE!" He ran into a different room and returned with an unknown tool. "Spike, would you mind if I took a few scales? For scientific research?" Tails asked, Spike nodded slowly and moved over to Tails who moved the tool towards him. Spike let out a quick yelp of pain when the tool plucked a few scales from Spike's hide.

Tails held one out at the rabbit who instantly attacked, the rabbit bit the scale in half and growled. Tails began backing up, while saying "So much for that idea." Twilight looked at him and said "Don't get so down on yourself, we're making progress aren't we?" Tails smiled before moving back into the kitchen and continuing to nibble at the sandwich. "So would you like for me to show you around town?" Twilight asked, Tails looked up and replied "Sure, I guess a break is needed. It just can't be too long, we need to get as much work done as possible."

Tails looked at the small and colorful town, he felt happy, just being in this place made him feel so. This would be the first he met Twilight's friends. She'd told him about them, but he never got a chance to meet them, it would also mean that his friends would see him for the first time in years. While excited he was also very nervous, would his friends freak out at him being here? No… Would they…? No... After all they were his friends, they would never do that. "First, we'll visit Sugar Cube Corner! The best place to get a tasty treat." Twilight explained, she led Tails inside and he saw the arrangement of sweets. Cakes, pies, muffins, but the most impressive looking were the cupcakes. Several different types, different colors, different flavors. Tails couldn't remember the last time he'd seen so many deserts. "Twilight!" A voice happily shouted, Twilight was tackled by Pinkie who was covered in flour and sugar. "Hi Pinkie Pie…" Twilight said between breaths. Pinkie got up, allowing Twilight to breathe freely. She turned to face Tails and said "Pinkie, I'd like to introduce you to Tails. He's Sonic's younger brother." Twilight explained, while Pinkie went wide-eyed at Tails. "He's so adorable!" She shouted before tackling him and shouting "Who's a little adorable fox? Who is? Who is? You are!" She was rubbing Tails like a dog, while he struggled against her.

"Twilight! Help!" Tails shouted, suddenly Pinkie was floating in the air, still making the rubbing motion, until she noticed she was off of him. Tails was still lying on the ground taking deep and heavy breaths. "Are you all right?" Twilight asked, while Tails grabbed onto the edge of a table and slowly rose. "Fine… I was just… Tackled by… A pink horse… Nothing to bad…" Tails muttered as Twilight set Pinkie down. "Pinkie, please try to control yourself. He's a guest, not a pet." Twilight said rubbing her forehead. "I'm sorry, he's just so adorable!" Pinkie shouted, while Tails braced to be tackled again. It never came so he opened his eyes, seeing Pinkie staring at him. "We just popped in to say hello, I'm showing him around town." Twilight explained before the decided to move on. "We can see Applejack next if you'd like." Twilight suggested. Tails nodded before they moved on to the farm that the Apple family called home. Tails tripped and landed in mud, covering the fox from head to toe. An apple flew over Tails' head, nearly hitting him, but he had ducked at the last second. "Almost! Don't worry Twilight! I'll save you from that monster!" Rainbow Dash shouted flying straight at Tails, he thought quickly and jumped into the air, spinning his two tails in the air like a propeller he managed to fly over Rainbow Dash, which distracted the mare causing her to crash into the side of a building. She recovered and launched herself at him, but Tails flew higher than her and landed on her back.

"What the!? Hey! Get off me!" Rainbow Dash shouted, while Tails held her wings down, forcing the two to plummet toward the ground. Before the moment of impact Tails, began to spin his tails, allowing them to make an almost smooth landing. Rainbow Dash fell into the dirt, making a small dust cloud, but she wasn't hurt, at least not seriously. "Rainbow Dash! Are you ok?" Twilight asked running over to her friend. Tails got off and began wiping the mud off his fur. "TAILS! What was that!?" Twilight asked him. "I was acting in self-defense. She attacked me first." Tails explained, rubbing the last of the mud of his fur onto the ground. "Sorry if I hurt you. I just tried to defend myself." Tails said walking back to Rainbow Dash who stared at him with shock. "Rainbow Dash I'd like for you to meet Tails. Sonic's younger brother." Twilight said, while Tails helped Rainbow Dash up. "Hi… How did you do that…?" Rainbow Dash asked.

"It's something I've always been able to do… I actually used to get made fun of it… Then I met Sonic! He took me on as his sidekick, and I learned not to care what other people think of me, as long as I have my friends!" Tails answered, turning to show his namesakes. Applejack had come out to see what the commotion was and saw Tails standing there with Twilight and Rainbow Dash. "Howdy Twilight. Yah need somethin'?" Applejack asked, walking over. Twilight smiled and replied "I'm just showing my brother in law around. He needs a break from his work." "Brother in law? You remarry already? You know they're workin' on a cure right?" Applejack questioned. "No! I don't think you understand! I'm Sonic's brother, you must be Applejack. Twilight's told me about you." Tails said, trying to fix the situation.

"So you're Tails? Sonic sure talked high an' mighty 'bout you." Applejack said with smile. "He did? What did he say?" Tails asked, now curious as to what Sonic had said. "He said you saved an entire city on your own. Even beat that Eggman guy!" Rainbow Dash shouted. "He had said you're his best friend. He can trust you through anything." Twilight added. "He said you never gave up on 'em. Always by his side no matter what." Applejack finished, leaving Tails feeling shocked. "He said all that? He didn't mention any of the times I screwed things up?" Tails asked. "Nope, but yah don't need to worry none. Everypony makes mistakes. It's all a part of life." Applejack said, turning and moving back inside the house. "Well, next we should see Rarity. I hope she's not too busy." Twilight muttered leading Tails back towards town.

"Oh, I must say you are simply the cutest thing I've ever seen! You're a like a little kitty! So fuzzy and adorable!" Rarity shouted, she was brushing out Tails' fur, it had become a mess and he hadn't combed it out in a few days. "OW!" Tails shouted feeling the brush hit a knot in his fur. "Sorry! Just need to do this quickly and…" Rarity had started, before quickly bringing the brush through the knot, ripping it off of Tails. "Oh! I'm sorry dear! Perhaps we should stop…" Rarity suggested while Tails stood up. "Thank you for at least attempting Rarity. I really appreciate the offer." Tails said rubbing the spot on his head where the patch of fur had been ripped out. "So you're Sonic's brother? Does Knuckles know you're here?" Rarity questioned, leaving Tails nervous. "No, he doesn't Twilight went to tell him, and I'm just waiting for her to come back." Tails explained, at that moment the door opened, and Twilight walked in.

"Well, Knuckles didn't believe me. He had to Gamma and Metal Sonic with something…" Twilight said, making Tails gasp. "Metal Sonic? What's he doing here?" Tails asked starting to look angry. "Gamma managed to reprogram him, so he's friendly now." Twilight responded, starting to lead Tails to where Knuckles was going to meet Gamma. He had been led to the outside of Applejack's barn, Tails could hear voices inside.

"Hand me wrench." Metal Sonic ordered, holding out a hand. Knuckles scanned the various tools and asked "Which one is that?" Metal Sonic let out an annoyed groan and asked "You don't work with tools much do you?" Knuckles shook his head and replied "Never had a need to. When you spend most of your time on a floating island, you don't really need tools… At least not beyond these." Knuckles lifted his fists into the air. "I would use a screw instead of a bolt there, it would hold together better." Tails said opening the door. "Tails?" Knuckles asked shocked. Knuckles grabbed the fox in a hug and shouted "Man! It feels good to see you again!" Then as if he had just realized what he was doing he dropped Tails and said "It's great to see you again." Metal Sonic looked up at him and said "Finally someone who know what they're doing. Tails hand me that wrench." He pointed a metal finger at a wrench sitting on a wooden crate.

Tails handed him the wrench and said "Look, I know you've supposedly changed, but don't think I'm just going to forgive you for everything you've done to us right away." Metal Sonic sighed and said "You may be his brother, but you are Sonic's polar opposite. Willing to trust without a second thought, reckless, hates sitting still. Then there is you. Very untrusting, you think too much, and you remain stationary for long periods of time." Tails wasn't sure if this was a compliment or an insult so he didn't reply instead he asked a question. "What are you working on?"

Metal Sonic looked up and replied "We're fixing up Omega, Shadow fucked him up pretty bad. I'm sure you've been told about the second invasion. Well Shadow was helping them, until Eggman tried to take over. Shadow worked together with Princess Luna and defeated the old quack. He banished himself. Making sure he wouldn't harm another soul. Amazing isn't it?" Tails was confused, what about any of this was amazing. "I… I'm not sure what you mean…" Tails said nervously. "The fact that this invasion happened only a month ago. This town had been burned to the ground, now look, almost identical. Same thing with other towns. Even Canterlot, amazing how fast this whole place was fixed up." Metal Sonic said while working on Omega. "Knuckles, go get Gamma. He should be here." Metal Sonic instructed. Knuckles nodded and left the barn to search for the robot.

"Listen… Tails… I know about my past… I know how miserable I've made your lives… I hope to make up for that. Whether you trust me or not is not anything I care about. I just want to make it up…" Metal Sonic said, twisting the last bolt in place. The barn doors opened, allowing Gamma and Knuckles to enter. Metal Sonic nodded as Gamma placed a small motor into Omega's chest, activating the robot. Omega's eyes began to glow with red lights, and he looked around the room. "Where… Am… I…?" Omega asked. "You're in a safe place." Tails replied, helping Omega onto his feet. "Tails? It has been long." "It has Omega… It has…"

* * *

><p>Celestia stood on the balcony, a guard approached and began to speak. "Princess… I have troubling news… Sonic, he has turned… He led the others… They've infected everypony in the research facility… He has a message for us…" The guard spoke, his voice shook with fear. "And…?" Celestia asked, waiting for the guard to speak. "He says… The Infected come."<p>

* * *

><p>There you go! Chapter 1 is complete! If you read the note above then you'll know that each chapter will now be around 5,000 words, but that includes the chapter title, and author's notes like these! I will be using OCs from the previous story. They will not appear until later chapter however. I will admit, that this will take longer to update, seeing as how I take my weekends off from writing. I will try to get enough to purchase Microsoft Word on my other computer so I can write on weekends. I'm going to try and take things more seriously because as I had mentioned in the last story (At what point I do not remember) I said I was going to be making a Wind Waker crossover, well there has been a change of plans… It will be taking a boss from that game, and he will find his way into Equestria… How will it be? You'll have to read and find out! I guess that's all for now, remember to leave a review telling me what you liked and what you didn't like. Yeah, that's about it so bye!<p> 


	3. Chapter 2

Chapter 2: Cloudanium (What ever happened to Shadow?)

Tails moved towards the throne room, he had been personally summoned by the Princesses, for what reason Tails didn't know. He slowly opened the large doors, peeking inside to check if the Princesses were present. "Tails I presume?" Celestia asked, startling the yellow fox. "Please, come in. Do not be afraid." Luna spoke softly, knowing that her voice could get extremely loud, which might scare the poor fox more. He opened the door fully and entered the room, he moved towards the Princesses and asked "You needed me? Did I break some law or something? If I did I'm really sorry!" Tails said, he felt nervous and didn't know what had happened. "No, no! Do not worry. We called you here to ask you a few questions is all. We understand that you and Twilight were working on a cure separately from the main research group, correct?" Celestia asked. Tails nodded, he felt a little more relaxed.

Luna began to ask the next question. "Have you made any progress?" Tails slowly shook his head before saying "I had a theory for a form of armor made of dragon scales… However the rabbit was able to bite through them quickly… I'm not sure if there is any substance stronger than dragon scales here…" Celestia frowned. "There is one substance, but gathering it is very dangerous… It can be found near Cloudsdale. You would have to get past a very dangerous beast, so I do not want anypony going after it." Celestia replied. Tails was curious but knew that he should let it go. "You know Sonic don't you?" Luna asked, making Tails feel a twinge of sadness. "Yes… I'm his brother… Not by birth… He took me under his wing as both a sidekick and a family member… My special ability helped him out a lot." Tails answered.

"Special ability? Could you show us?" Luna asked, leaning forward. "I guess… I mean it's nothing special…" Tails muttered before spinning his tails quickly, he felt his feet leave the ground and knew he was airborne. Luna and Celestia were shocked at this sight, a literal flying fox. "That's incredible… You may actually be able to set foot on Cloudsdale." Luna said, her tone was void of emotion, not from fear or depression, but from awe. The small fox landed, he seemed confused about something. "What do you mean?" Tails asked, raising an eyebrow. "Only creatures with the ability of flight can walk on the clouds that make up the floating city… If you will… We might find out sooner or later…" Luna answered, while Tails began to shuffle nervously. "Do not worry, we are almost finished. Are you aware of the latest events?" Celestia asked. Tails shook his head, the two Princesses exchanged uneasy glances. "Sonic… Had turned… He plans on leading these… Infected… On an attack against all of Equestria." Luna answered, Tails was shocked. He couldn't believe what he had heard. "This can't be true! It has to some form of cruel, cruel joke!" Tails shouted, beginning to back away from the royal sisters. Celestia frowned and replied "I'm sorry… It isn't. We aren't sure when he hill attack but his threat has been made clear. We need to prepare for war if it comes to that… It seems war is more common these days… Eggman… The Changelings… Now… These zombie like creatures…" Tails turned and ran, the Princess called after him, but he didn't even glance back. Celestia could see something glinting in the light behind him, the tears hit the floor, leaving small wet spots. "I'm worried about him… He might do something foolish…" Luna said, her tone was sad. Celestia stared at the place he had once been, and then began to whisper "We've reduced him to nothing but a scared child, searching for comfort in the cold, dark, world full of danger…"

* * *

><p>Tails stood next to Rainbow Dash, Twilight, Speedy, and a Pegasus who knew Twilight. He had a tan bag that was strapped over his shoulder. "Tails… I'm not sure this is smart… I mean fighting the Cloud Guardians just to get a material… Doesn't really sound like a good idea…" Twilight said, looking at the yellow fox. "You said they attack ponies right?" Tails asked, getting a nod from Rainbow Dash. Rainbow Dash was scowling, she faced a section of the clouds and said "They attack anything that they feel like attacking, not to mention they mess with the weather a lot, which makes the Pegasus reputation bad!" Tails looked straight ahead, he then said "That's enough for me. Sounds like taking these things down would be doing everyone a favor." Twilight walked in front of him and shouted "We don't even know if you can step foot on clouds!" Tails smiled before saying "We're about to find out." Tails began to fly off towards a nearby cloud, he floated above it, gently lowering himself until he felt his feet the cushy surface, he stopped spinning his tails and let out an excited cry. "I can walk on clouds! I can! I can! This is amazing!"<p>

Tails began leaping from cloud to cloud, grabbing onto the edges, pulling himself up, and leaping to the next one. "WHOO! YEAH! THIS IS EPIC!" Tails shouted, until he noticed the others ahead. "You ready to find these things?" Rainbow Dash asked, getting an arrogant nod from Tails. Tails began to fly and moved along with the others. They searched for about ten minutes when Rainbow Dash noticed something. Tails was starting to fall behind in the group, he was panting and covered in sweat. "You all right?" Rainbow Das asked, getting no response from the young fox. He landed on a nearby cloud and collapsed onto his stomach. Rainbow Das rolled her eyes before moving over to Tails. "You tired already?" She asked, poking the fox with a hoof. "I've never… Flown this… This long… Without… Without a… Break…" Tails said between breaths, his eyes were shut, but not tight. "You want me to wait…?" Rainbow Dash asked, landing on the cloud.

"No… Go ahead without me…" Tails said, filling his lungs with air. Twilight, Speedy, and Star Mane, as Tails learned her name was, had landed on a nearby cloud and watched. "Maybe we should all take a break…" Twilight suggested, which made Rainbow Dash groan in frustration. Twilight had a pair of satchels and opened one, pulling out a bottle of apple cider. "Is that…?" Rainbow Dash asked, feeling her mouth start to water. Tails sat up and began digging around in his own bag, he pulled out a bottle of water and began to drink. "You want to take a break now?" Twilight asked, smiling at her friend.

* * *

><p>A single figure walked through the forest, he cut apart branches with a machete, and he heard a growl and dodged an attack made by a decomposing pony. He frowned and swung the machete decapitating the pony in a single motion. The pony's body rose onto its feet and placed the neck stump near the head, the muscle began to grab onto each other, pulling the head back onto the body, the muscle began to mend, he let out a gasp and accepted that he had only on option. As much as it pained him to do so he ran, he ran until a hiss broke him from his concentration. A Cockatrice glared at him, it stared dead on, but nothing happened. He had spent a long time in this forest, he found he was immune to many things, one of them being the stare of a Cockatrice. It began to back away when it realized its gaze had no effect. He quickly slaughtered the beast, its blood covering his blade and the ground. He heard the growl again and turned to face the pony. It moved closer to him, until it stepped in a puddle of Cockatrice blood, it yowled in agony, as bits of its leg began to fall off, melting into a gray slime. He rushed forward and sliced the pony's throat making fall to the ground, slowly melting into a gray goo. He looked at the blood then at his blade. He knew this might have been of some importance, but he'd have to research it first. The Dark One moved through the forest again, searching for another Cockatrice.<p>

* * *

><p>Tails finished the bottle of water and the sandwich he had brought with. A little picnic in the sky. Tails looked at the others and saw them still enjoying their apple cider, and food. He placed the empty bottle in his bag and brushed the crumbs off his lap. "Any time you're all ready to go!" Tails shouted, giving them a thumbs up. Twilight emptied the bottle of cider and placed it in one of her satchels, before looking at Star Mane, Rainbow Dash, and Speedy. "Uncle Tails?" Speedy asked, getting Tails' attention. "Yes?" Tails asked, looking at his niece. "Is this going to help Dad?" She asked, gazing up at him with her miss matched eyes. "It'll help <em>us<em>, so we _can_ help Sonic." He replied, looking off at the sea of clouds ahead. "Does anyone even know what these things look like?" Tails asked, placing his hands on his hips.

"Well, there are four in total. Stormus, the lion of rain. Clapus, the crocodile of thunder. Flashus, the shark of lighting. Then the leader, Cloudus, eagle of clouds." Rainbow Dash said with pure excitement in her voice. "How do you know all this?" Tails asked, perplexed at how Rainbow Dash would know so much about ancient creatures. "It can all be found in Daring Do and the battle of the Cloud Guardians." Rainbow Dash replied, she gasped and pointed out where a pure white fin was poking out from the clouds. "THAR SHE BLOWS!" Star Mane shouted, with a goofy smile on her face. "Technically that was used when a whale is spotted." Tails said before noticing the fin was moving towards them. The large shark jumped out of the clouds, that's when Tails noticed why it was one of the Cloud Guardians. Its entire body was made from clouds, its eyes however were a deep ocean blue. It let out a loud roar before diving into the clouds, and disappearing beneath them.

"We need to keep our eyes peeled. It could be anywhere!" Tails shouted. He then saw the fin rise from the puffy "water" it was moving at a steady rate towards them. Tails waited as it jumped at him, teeth flashing ready to devour the young fox. Tails jumped onto the back of the beast and felt it jerk around wildly. "Tails?! What are you doing!?" Twilight asked, she was clearly in distress. Rainbow Dash attempted to tackle Flashus, but was smacked away from the shark's giant tail. Tails took his knowledge about regular sharks and did the most logical thing. He jabbed his pointer and middle fingers into its right eye, making it yell in pain. It tried to fling him off, jerking and throwing its body in every possible direction, but Tails managed to keep his hold on it. Flashus let out a roar before diving into the clouds, taking Tails with him. It was impossible for Tails to see through the clouds, he would have to wait for Flashus to surface. Flashus broke the surface of the clouds and Tails shifted his weight to his left side so he was leaning to his left. Flashus looked at Tails and was soon fully blinded when Tails' fingers once again were jammed into its eye socket. Flashus fell onto its side, sitting on the clouds, taking heavy gasping breaths. Tails began to run past it, leaving Twilight, Rainbow Dash, Speedy, and Star Mane rushing to catch up. Tails avoided the talons of Cloudus, which nearly grabbed him by the head. He kept running though, when a single thought came to mind. _SHIT! I don't even know what this stuff looks like! How can I find it!?_ He ran past Clapus who snapped his jaws together making the loudest thunder clap Tails had ever heard. He had to cover his ears while Clapus snapped his jaws repeatedly, making the sound over and over. He noticed something peculiar ahead it was small clouds, however they were a forest green. He grabbed one and threw it behind him. It hit Cloudus dead on, and an audible _CRACK_ could be heard.

Cloudus began to wobble, she was unstable making her crash into the clouds below. Tails still ran on, not looking back for anything, he was soon confronted with Stormus who charged at him. Tails jumped over the lion and kept running. He heard sounds of fighting and dared to take a peek behind him. He the four guardians lying in a pile, with Rainbow Dash, Twilight, Speedy, and Star Mane waiting. "Thanks guys… I don't think I could have ran much longer…" Tails said nervously. _"Might warriors… You have proven yourself worthy of the Cloudanium…" _Cloudus spoke, her voice was smooth and beautiful. _"However you must decide which one is the real Cloudanium… Should you choose wrong you will be slaughtered immediately…" _Cloudus added, making five large different colored clouds appear. _"Choose wisely…"_ She said to the group. Rainbow Dash flew in front of her and said "I have a better idea…" She turned around and bucked Cloudus in the face knocking her out. "Grab the clouds! Quick! Grab the clouds!" Rainbow Dash ordered, the group didn't hesitate and each one grabbed a cloud. "Now let's get out of here before they wake up." Rainbow Dash said flying off with the others following close behind.

* * *

><p>Tails was in the library, he inspected each of the clouds carefully. "Red appears to be some form of hard candy, strawberry… Yum! Blue is nothing but water… Purple is just a regular cloud colored… Yellow is very sticky, but has a nice lemon flavor… That means green must be Cloudanium!" Tails shouted he smiled and attempted to break the material. He found that his current tool couldn't shatter the metal. He let out a loud sigh and looked through the large selection of books searching for the material. He threw several books across the library floor, he hadn't found anything but he wouldn't stop searching. Spike entered the room and felt anger rise in him. Tails was very nice to the young dragon but one thing he didn't do was clean up the books he flung across the room in his search for the right piece of textual evidence. Spike was expected to clean up the mess that was his job after all. He began picking up after Tails, placing each book in its proper place. "I clean up all the time and I never get a 'Thank you Spike.' Is that so much to ask for?" Spike grumbled to himself. He watched as Tails looked through book after book, trying to find the information. "Why don't you call Gizmo? He might be able to help." Spike suggested, making Tails look up. "Great idea! Spike could you get him for me? Please?" Tails asked, the small purple dragon rolled his eyes before moving for the door. "Don't worry I'll clean up the mess." Tails shouted after him. Spike smiled before stepping out into the town.<p>

Spike walked through the town until he found himself at a green house. He moved forward and knocked on the door, he could hear metal clanking as somepony came to answer the door. "Just a second! I'm almost there!" Gizmo shouted from inside the door. Gizmo opened the door and looked at the small dragon. "Spike! How you doing my little buddy? Please come in!" Gizmo said stepping to the side allowing Spike to enter. Spike noticed the various metallic machines around the house and felt uneasy. "Sorry about the mess. My latest invention didn't work out so well… Let's move into the living room, it is a lot cleaner in there." Gizmo muttered, leading Spike through the metal clogged hall. They entered a room with green wallpaper, a large fireplace, and two comfy looking chairs. Spike noticed a picture on the wall and asked "Who is that?" Gizmo looked at the photo and smiled. "That is my great, great, great, great, great, great, great, great, great, great Grandfather. Gizmo Inventington the seven thousand and twelfth. All the sons in the family were named Gizmo Inventington, it's sort of a family tradition." Gizmo explained making Spike gasp. "You're an Inventington!? One of the richest families in Equestria! The only one richer than them is Filthy Rich himself!" Spike shouted.

Gizmo sighed before saying "That's why I didn't tell anypony… Once ponies began finding out that I was an Inventington they treated me better than they did before all because of my family's money." Spike frowned before saying "Gizmo, it doesn't matter what amount of money you have… Think about all your family has done! All the things they've invented!" Gizmo looked up and said "It doesn't matter… Promise me you won't tell anyone…" Spike nodded and began to explain why he had come to visit. "Tails needs my help? Well let's not keep him waiting!" Gizmo shouted, rushing out of his home. Spike followed with a large grin on his face, he had met an Inventington.

* * *

><p>The Dark One found himself at a shack. <em>"What's this doing in the middle of the Everfree Forest?"<em> The Dark One wondered. "Back stranger go away! You will not harm me today!" A voice shouted, making the Dark One turn. A Zebra stood there, she was glaring at him. "I'm not going to hurt you. I'm just wondering why you would choose to live in a place as dangerous as this." The Dark One responded. The Zebra seemed to calm down, but she said something that startled the Dark One. "Through the doom and gloom you wallow… I'm surprised to see you out here, Shadow." The Dark One took a step back and asked "How do you know my name?" The Zebra moved forward and said "It is known throughout all the land, the one who gave the Changelings a hand. You went into self-exile, but the ponies of towns haven't spoken of you in a while. Zecora is my name, brewing potions is my game." Shadow looked at Zecora and sighed. "I apologize for scaring you. I don't suppose I could stay with you could I? My attempts at shelter are almost always destroyed, or I have to move on due to wild animals."

Zecora nodded and said "You may stay as long as you want, just the wild animals try not to taunt." Zecora said with a smile. "I can find some way to help you." Shadow said, Zecora seemed to think before saying "Perhaps your form of rent, will be fetching me he occasional ingredient." Shadow let out a nod before Zecora opened the door to her home and led Shadow inside.

* * *

><p>Gizmo and Tails began moving the metal spike towards the Cloudanium, it made contact but didn't break the substance, making the two groan in anger. "We've tried everything!" Gizmo shouted, he looked at Tails who stared at the green cloud. "Wait! We need a pegasus!" Tails suddenly shouted, running out of the library. He returned a few moments later with Rainbow Dash who had been woken up. "Did you really have to interrupt my nap? This had better be pretty important!" Rainbow Dash shouted her mane was a mess, but she didn't care. "It is! You said Pegasi had the ability to control clouds right?" Tails asked getting a nod from Rainbow Dash. "Well then you should be able to break the Cloudanium!" Tails finished. Rainbow Dash looked at the green and bucked it, the cloud shattered like glass, revealing something inside. It appeared to be a glowing gold metal that was already in ingots. "The cloud was a form of chest! How did you figure it out?" Gizmo asked, Tails smiled before saying "It sounded hollow when we tried to break it." Gizmo smiled before muttering "There's enough here to make a full set of armor for seventy times seventy amount of soldiers in Canterlot!" Tails grabbed one of the ingots, it was surprisingly light. He held it out to the rabbit, it bit down on the ingot and whimpered in pain. The rabbit let go of the ingot and its teeth then fell from the mouth.<p>

Tails reached out a hand to the rabbit and felt its gums attach to his hand. "Harmless now… The real question is… Will we have time to make enough?" He asked looking up at the others who as well looked around nervously. "We should get started right away then." Gizmo said quickly, he got nods from everyone and they began to lift the light ingots and make some armor.

* * *

><p>Sonic moved forward, he led the group of Infected, they marched through Canterlot, not harming anypony, but the streets were deserted. Sonic moved towards the castle, the guards let him pass, fearing to become one of them. Sonic pushed open the doors of the throne room, startling the three Princesses and the captain of the royal guard. "Hello, did you all miss us?" Sonic asked, walking forward. "Why are you here Sonic?" Luna asked, she glared at him not once taking her eyes off his movement. "Relax Luna. I'm not here to hurt anyone… At least not yet." Sonic said his cocky smile changing into an angry frown. "Then why are you here?" Cadence asked, she look worried, not scared. "To negotiate. I've infected how many of your people Celestia? About three thousand? This could all stop, the pain, the wars, the death…" Sonic replied with a grin. Celestia looked at him and saw the changes where horrifying. The fangs that prevented his mouth from closing, she could see his heart it was beating signaling that he was alive, she saw his eye it had become a reptile like slit.<p>

"Explain." Celestia ordered. "You obviously don't want to go to war again. You don't want them to suffer. You don't want anypony to die. I can make all that stop. You just need to join us willfully." Sonic said, telling the details. "Never!" Celestia shouted. Sonic began to laugh. "You really think this will get you on our good side?" He asked. "Leave. Don't ever return!" Celestia shouted, getting onto her hooves. Sonic now was angry he stood and moved closer to the princess before saying "You've just dug this entire city's grave." He then turned and walked out from the room with the others following.

* * *

><p>Tails placed on the armor and moved forward. "Lightweight… Easy to move in… We may have done it! The perfect armor to use!" Tails shouted. "That would depend… How many bites will it take to break the armor?" Gizmo asked, getting some nervous glances. "We'll have to cross that bridge when we get there." Tails replied, taking off the armor. "Now what do we do?" Gizmo asked. "We work on a cure." Tails replied.<p>

* * *

><p>Shadow moved through the forest, he avoided the Manticore's claws before kicking it in the jaw. "Back off!" He shouted, while the beast reared back and pounced at him. Shadow took the green Chaos Emerald and shouted "CHAOS CONTROL!" He disappeared in a flash of blue light and reappeared behind the beast. He landed on its back and grabbed the mane, yanking upwards. The Manticore yowled in pain as it ran forward. Shadow jumped off as the monster hit a tree, causing a large bee hive to fall on its head. The hive shattered, scattering larva, chunks of the hive, and globs of honey in several different directions. The adults swarmed the beast, it roared in agony before running off into the deep forest. Shadow looked at the broken hive and held up a list. <em>Green Honey<em> was written there, he bent down to get a better look at the substance. It was a shade of light green, almost the color of the Chaos Emerald he owned. He took a wooden bowl and scooped a small amount of the honey into it. Shadow watched as a deer emerged from the woods, it stared at him but realizing that he was no threat moved closer to the fallen hive. It stuck out its tongue to lap up the leftover honey. "I wouldn't if I were you." Shadow said to the animal.

The deer licked the sticky green substance and quickly back away gagging. It took heavy breaths and began to wobble. Its knees shook before it collapsed still taking the heavy breaths which were now slowing. Shadow rolled his eyes and moved to the fallen deer. He had a small sack with him, opening it he placed a small purple leaf in his mouth. He chewed until it had become a paste, he then spit it into his hand and placed it into the deer's mouth. The deer began to take slow shallow breaths as it started to recover. Shadow stood up and began walking away, he had remembered Zecora's warning. _"This honey you must not taste, your throat will swell without haste. Making it hard for you to breathe, to stop it eat this purple leaf. Chew it until it is a paste, then your life you will not waste."_ He couldn't help but smile. Zecora showed no fear of him, no matter what he did she seemed to mind him none. He noticed the animals didn't really mind him either, of course he was speaking about the non-predatory animals. The Manticores, Cockatrices, and various other creatures still saw him as an enemy, they attempted to attack him on sight.

Shadow moved through the thick plants, and found himself at something very peculiar. It appeared to be some form of container made entirely from stone. He grabbed and edge and began pushing, it was heavy even with his amazing strength. He pushed it off and heard the stone slab break, bits of rubble skittered across the ground. He looked inside and saw what appeared to be a skeleton. It wore a lot of jewelry, almost the same style as Zecora wore. _"Is this some form of grave?"_ Shadow asked himself, until he noticed the bracelets and a necklace that were different in color. They were black and red, the bracelets had symbols that made something in his mind stir. The necklace had several different charms on them, very familiar charms. He gasped as he realized they each were something he had seen before. The symbols on the bracelets was his own symbol, the one he had adopted from the Black Arms. The charms matched those that Black Doom wore exactly. Even the tattered clothes on the skeleton resembled Black Doom's robes. He reached inside the stone coffin and removed the bracelets.

He removed the golden rings from his wrists and placed them on the Zebra's stomach, or at least where the stomach should be. He put the bracelets on and began to walk away. _Shadow…_ A raspy voice whispered. Shadow turned to see the skeleton was sitting up. _Brother… You have arrived…_ It spoke to him. Shadow took a step back and stared. _Brother…? You do not speak…? Is something wrong…? _Shadow found his voice and shouted "Who are you? How do you know my name?" _I am one of you… One of the Black Arms… They have watched this planet from afar…_ Shadow was shocked he then asked "What do you mean?" _I was created by our father… Black Doom…_ "He is NOT my father! He is one of my ancestors, but not my father!" Shadow shouted. _I am one of you… You can keep thee bands… They will increase your power… We need only wait for father to come…_ It began to crumble into a cloud until it was nothing but dust blown away from the wind.

"What did he mean? Wait for Black Doom? Impossible… I killed him… I need to get back to Zecora. She needs this green honey…" Shadow said with a shake of his head. He moved towards the location of Zecora's shack, knowing that something horrible would happen in the future. He found Zecora standing outside of her house, she looked at Shadow worriedly and asked "Shadow, are you all right? A spirit has given me a fright." "What do you mean?" Shadow asked. "A strange creature who claimed to know you. Shadow what should we do?" Zecora asked. Shadow stared in the distance, he could swear that he had seen something move. He shook his head and replied "Nothing, for now. I got you that green honey."

* * *

><p>Hey all, just wanted to apologize for the long gap, I just wanted to spend Thanksgiving relaxing with my family. After that I wasn't well… But I've gotten this chapter done and it is time for an update. My Wind Waker thing will not be created due to me never having completed the game and my copy of the game breaking. So instead I will be publishing a different crossover. I am a fan of the show "Hero 108". They had all sorts of different animals, but not a single hedgehog. You all know by now that Sonic is a king… Can you see where I'm going with this? For those of you who do… Congrats! Look out for "Hero 108: Rise of Chaos"!<p>

Another little side note, I have been getting complaints about Pokémon Mystery Dungeon Gates to Equestria. It is currently on hiatus, I need to work on some other things first, so don't worry I will be working on it again. What else is there to say now except I really appreciate all the support I'm getting for this story! I'm going to be making a fourth story in the Chaos and Discord series! BYE!


	4. Chapter 3

Chapter 3: Shadow's Return to Ponyville

Shadow sat in the small shack, he attempted to get on his feet, but felt pain flood through his body. "Shadow I keep telling you, this is not a common flu." Zecora said to him. Shadow ached all over, he had caught something while he was out searching for the green honey. "You'll need plenty of rest, sleep now Shadow that would be best." Zecora said, while Shadow began to close his eyes. Shadow soon found himself asleep, plagued with nightmares that haunted him.

* * *

><p>"Shadow… Please… Help me…" Maria said as her blood ran across the floor. Shadow ran to her and tried picking her up. He found that no matter what he did his hands moved through her like he was some kind of ghost. "Shadow… Please… Please…" Shadow bent down onto one knee he rest his hand on Maria's head and began stroking her. "Maria… I'm sorry… There's nothing I can do…" Shadow said, he felt tears drip down his face. "Shadow… Why do you hate me…?" Maria asked, shocking the black hedgehog. "I don't hate you! You mean more to me than anything else!" Shadow said, getting a sick feeling in his stomach. "Fine! Then I hate you too! If you cared about me… You'd have… Done… Something…" Maria said as her eyes slowly shut. "Maria!" Shadow shouted, hearing a laughing behind him. Hundreds of Black Dooms moved towards him, Shadow got onto his feet and prepared to fight. However each attack he made did nothing, the Black Dooms remained unharmed and then began their assault. They attacked Shadow, hitting him with energy, meteors, and many other forms of magic. Shadow fell onto the ground and looked up at Black Doom, who lifted a large stone and dropped it onto the hedgehog.<p>

* * *

><p>Shadow woke covered in sweat, he looked around the room rapidly, and found no sign of anyone. He got onto his feet despite the burning pain, and began to search for Zecora. "Zecora? Are you here?" Shadow asked but heard a voice say "Shadow! Shush! They are near! If you speak too loud then you they will hear!" Shadow got onto his hands and knees before crawling over to the source of the sound. Zecora was hiding underneath a table, and Shadow crawled under there as well. "Who will hear us?" Shadow asked, but heard someone speak. "Come out, come out, wherever you are… Don't you want to join us?" Shadow peeked out and saw another one of those zombified ponies. "Another one?" Shadow asked, as quietly as he could he reached for the top of the table. He searched with his hand until he felt the handle of his knife. He grabbed it and yanked his hand into cover as the pony looked in the direction. "You said there was a cockatrice nest nearby?" Shadow asked, getting a nod from his Zebra companion. "Good. We'll need it." Shadow crawled out from the table, moving nearly silent he managed to sneak up on the pony and dug the knife into its skull. The pony let out gasps of pain and surprise as it slowly began to dissolve into the gray liquid.<p>

"Cockatrice blood kills them, nothing else will. I cut one of their heads off and it reattached." Shadow explained. Zecora and Shadow began packing some things, items and objects they would need for the journey to the nearest town, which just happened to be Ponyville. "Got everything?" Shadow asked. Zecora nodded before the two left the shack, heading towards the nest to collect the blood.

* * *

><p>They moved past the now empty nest, bottled cockatrice blood had been added to their bags, and their guard on its absolute high. "We should be near town…" Shadow muttered when Zecora cried out in pain. He whirled around and saw a plant had dug some form of teeth into her leg. Shadow severed the plant's stem and grabbed onto the "head" before forcing the jaws open. They both looked at the wound and realized it was deep. Shadow could see the bone through the wound, so she was lucky it didn't snap any of them. Shadow heard bushes shake and rumble as a Manticore approached. "Shadow go on without me… I'll wait for my death in this pain and misery." Zecora said between gritted teeth. Shadow picked her up bridal style and began to run, after a few moments his shoes activated allowing him to float above the ground.<p>

Shadow heard the Manticore continue chasing them, no matter what it just kept following. "It must be her wound… A predator will almost never refuse an easy meal…" Shadow thought, still hovering away from the large predator. Shadow saw bright light seeping through the thick forest bushes and trees, meaning the way out was straight ahead. "We're going to have to break through the bushes, so this may hurt!" Shadow shouted, bracing for impact. Zecora went to protest, but she felt branches whip her, leaving visible red marks. Shadow had taken most of the abuse, turning so that his back faced the bushes, the branches digging into his back drawing blood. Several ponies gasped at the sight of a hedgehog and a zebra bursting through bushes, some ran, others stayed to investigate. "Zecora?! Are you all right?" Twilight asked, while Tails, Knuckles, and Rarity followed. Zecora lifted her head and looked for Shadow, she saw him lying on the ground in a shallow puddle of blood. "Please, you have to help us… Help quickly without a fuss…" Zecora said attempting to get up. Twilight stopped her and asked "Knuckles, can you take her to a hospital?" Knuckles nodded before heaving the zebra over his shoulder and moving towards the hospital. Twilight looked over at Shadow and frowned. She walked over him and he began to lift himself with his arms. "I should've known you'd have something to do with this." She said to him. "Good to see you too…" Shadow muttered before spitting out blood.

"What did you do to her?" Twilight asked, getting on eye level with the black hedgehog. "I rescued her… Some kind of plant attacked her… I carried her through the forest, while being chased by a Manticore." Shadow had begun to glare at the princess, knowing that she would like nothing more than for him to die. He had been responsible for millions of deaths if not more. Shadow waited for a response but one never came. Twilight was staring at something in the distance. Shadow turned his head and saw what she was looking at. A mirage or at least he hoped it was one. Sonic stood there, he had his same cocky grin. Only he was different, his left eye was missing, pieces of him had fallen away, but Shadow could see his heart, it beat in a steady pace. Shadow blinked and Sonic was gone, Twilight looked at the black hedgehog and helped him onto his feet. "Like it or not… I'm going to have to trust you…" Twilight said with a frown.

* * *

><p>Tails sat in the library with Star Mane and Gizmo. "Hand me that beaker." Tails instructed. Star Mane crossed her hooves and replied "No." Tails looked at her and asked "NO!? WHY NOT!?" "You didn't say please." Star Mane answered. Tails sighed before saying "PLEASE hand me that beaker." Star Mane appeared to think about this before saying "No." "What!? WHY!?" Tails asked furiously. "It'll be too late." Star Mane replied. Tails slammed his fists on the table, spilling the chemicals on the floor and the desk. "See." Star Mane said. Tails looked at her and asked "Why are you even here? You're more interested in space and such right?" Star Mane nodded before saying "I was bored. I'd also heard something from Knuckles… What is the 'Spruce Monopoly Arf'?" Tails asked "You mean the 'Space Colony ARK'?" Star Mane nodded, and Tails smiled. They heard the door open and they assumed it was Twilight so they continued with their conversation. "To tell you the truth I don't know that much about the ARK, you'd have to ask Shadow… Who knows here he is…" Tails answers but a voice began to take over the conversation.<p>

"The ARK was my home. Hundreds of humans were onboard… Then the lead scientist, Professor Gerald Robotnik created me with the assistance of an alien being known as Black Doom. Black Doom tried to destroy Earth, and he manipulated me into assisting him. However Prof. Gerald knew that Black Doom would return so he attempted to build the Eclipse Cannon. A part of the ARK that fires a beam of energy powerful enough to pierce stars. Then a government agency known as G.U.N. mistakes the Eclipse Cannon as a weapon to be used against them. G.U.N. stormed the ARK killing anyone who stood in their way. I was then discovered and set as a primary target to be eliminated. A young girl was in danger as well, I had to help her escape. We managed to get a room that would allow us to escape to the planet below… But she was killed in that room… I couldn't save her… I had destroyed a monster that bonded with the ARK, I couldn't have done it without Sonic's help…"

Tails looked at Shadow and asked "Shadow? What are you doing here?" Shadow sighed and said "I had to help Zecora escape from those zombie like monsters." Tails noticed the bandaged that were wrapped heavily around his torso. "Did they get you?" Tails asked, while Shadow laughed. "No, a bush cut the fuck out of me. Zecora was lucky she only some marks." Shadow explained. "Well it's good to see you again." Tails muttered, giving a small smile. "Same here buddy." Shadow said with a grin.

* * *

><p>Sonic picked up the file, it was the cartoony type. The kind you'd see someone break out of prison with. He brought it to his fangs and began to file. He had to do it, he had to. He filed them down despite the pain that it caused. He stopped when he was able to close his mouth, despite this he still had the fangs. "Man this feels so much better. Who's next?" Sonic asked, holding out the metal file. Scourge took it and began to copy the process. He held it out to Trixie who used magic to file them down. Silver then took it and filed his own down, before assisting Fluttershy and Applebloom. Sonic smiled and moved his jaw a few times, he heard it crack and he laughed. "That felt great!" Sonic shouted. "Now what? The Princesses have refused us… Do we attack?" Silver asked. "Not yet… We will eventually… Until then… We grow our numbers…" Sonic said with a wicked grin.<p>

* * *

><p>Shadow sat outside of the library, he was doing something that he didn't do very often. He placed the cigar in his mouth and lit a match. He lit the cigar then quickly shook out the match while got strange looks from the occasional passerby. "Shadow. I believe Zecora is… Are you smoking?" Twilight asked, looking at him. "Yeah. So what?" Shadow replied. Twilight sighed in annoyance and asked "You know that's not healthy right?" "Yeah. After all I've been through I need this…" Shadow answered, he held one out to Twilight who looked confused at the motion. She figured it out and began to speak quickly. "Oh! No thank you… I don't really want any of your cigars… Not because of you! I just don't smoke! It has nothing to do with you!" Shadow placed the cigar back into the bag he carried and blew out smoke. "You don't need to worry. I'm not going to kill you over your opinion on me. I may maim you but that's another story." Shadow said playfully nudging her.<p>

Twilight was a little nervous, something about him was hard to tell if he was joking or not. "So you were saying something about Zecora?" Shadow asked. "Yes, Zecora should be able to leave the hospital today, and you two are welcome to stay in the library as long as you need." Twilight finished her earlier started report. "I can't say I know why you're treating me so nicely… I killed hundreds… Thousands… Millions of innocent ponies… I can't really do anything but thank you…" Shadow commented, making her feel shocked. "Everypony deserves a second chance… Even if you aren't a pony…" Twilight said. Shadow nodded and looked at her. "Cockatrice blood kills them… The Infected… You know that if I have no other choice… They will have to be killed…" He said, she nodded grimly and began to walk away.

Shadow put out the cigar and dropped it onto the ground. He walked towards the hospital and entered. Zecora was walking for the exit when she spotted him. "Shadow, I just don't know how to thank you… Perhaps there is something I can do?" She asked him. "Don't worry about it, I was just helping a friend." Shadow replied, he placed his hand under her chin and looked into her large turquoise eyes. Shadow turned and began to walk away. He hadn't noticed that Zecora still stood there in a daze.

* * *

><p>Tails looked back at Star Mane was had been tied to a chair, something Tails didn't want to do but was forced to in order to actually get some work done. "Gizmo hand me the blue beaker." Tails ordered, getting the blue beaker placed in his hand. Tails narrowed his eyes as he tried to pour a single drop into the green chemical. Tails watched the drop lengthen as it went to break away from the beaker's edge and fall into the green solution. Suddenly the door was flung open, causing Tails to jump, the entire bottle was poured into the green solution and it began to fizz and bubble quickly… Tails' eyes widened as he shouted "OH FU-!" He was cut off by the explosion, he was flung across the room and landed on his back. He looked at the destroyed desk and let out a whimper of sadness. "Three weeks of research… Three weeks…" He muttered as a smiling Pinkie Pie came into his view. "Tails! I need to give you something!" She shouted dropping a pink envelope onto his ash covered lap. He picked it up with his now blackened gloves and opened it. Inside was a card that read "You're invited!" Tails was confused, so he opened the card. "Dear Tails, You are invited to your 'Welcome to Ponyville' party! There will be games, food, and lots and lots of fun! See you there! From, Pinkie Pie." Tails looked up at the pink mare and groaned. "I'm sorry Pinkie, I just don't have the time. We need to find a cure as quickly as possible. Maybe another time." He said with a forced smile.<p>

Pinkie looked sad and her hair deflated like a balloon, it went flat down at the side of her head. "I've already sent out the other invitations… I've got all the decorations and food out… Please?" She asked starting to get teary eyed. Tails let out a sigh of defeat and said "All right… When is it…?" Pinkie suddenly cheered up the tears disappeared and her hair went back to normal. "Later tonight! See you there!" She shouted happily. She bounced out of the room, leaving Tails sitting in soot and a clutter of books. Star Mane managed to get the rope out of her mouth and inhaled deeply. Tails looked at her as she began to ask questions about his home and other things in an endless strain, not giving him time to answer a single one of them. Tails simply sat there as his right eyelid began to twitch.

* * *

><p>Shadow and Zecora walked towards the barn, that's where the invitation said to meet, and he wasn't going to question it. He heard hushed whispers as Tails, Knuckles, Metal Sonic, Gamma, and Omega joined the two. Shadow pushed the barn door open and they were greeted with a loud "SURPRISE!" Almost everypony in town was there. Pinkie was in the front of the group, she had a large grin on her face. "Come on in!" She shouted, prompting them to enter. Shadow couldn't help but smile at this. He walked in with the others following and the party then officially began. Pinkie had ushered Shadow and Tails to a game that was familiar. "Pin the Tail on the Donkey!" Pinkie shouted. "I've seen human children play this before, but I never saw what the interest in it was." Shadow said, Pinkie giggled and wrapped a blindfold around Tails' face. "What the…?" Tails asked startled. She spun him quickly and grabbed him, forcing him to stop.<p>

Tails moved forward and placed the pin on the target. Pinkie removed his blindfold and he saw that he had missed. "Your turn Shadow." Pinkie shouted, wrapping the blindfold around his face. "Let's make this a bit more interesting. I'll do it with one hand behind my back…" Shadow started. "I don't see how that makes anything more interesting…" Rainbow Dash muttered. "Facing backwards." Shadow finished getting some reactions from the crowd. Shadow was spun around, then he placed one hand behind his back. Instead of walking backwards, like all thought he would, he threw it backwards, striking the target dead on. Pinkie took off the blindfold and showed Shadow that he had gotten a perfect hit. The crowd cheered for him, and he gave a small bow. Shadow moved around the party and saw a table of food, lots of sweets filled the table nearly covering the entire thing. Shadow smiled and took a single chocolate cupcake with dark red frosting. He took a bite and was flooded with memories.

* * *

><p>"Hey Shadow. Guess what I made." Maria said to the black hedgehog. "What?" Shadow asked, Maria let out a few giggles before revealing in each hand she held a single cupcake. They had dark red frosting neatly placed on the top. "Here." Maria had said thrusting out her hand to Shadow. He took the cupcake that she had held out to him and smiled. Shadow looked at Maria and took a bite. "I think I might have burned them a bit." Maria confessed. Shadow was trying his best not to gag on the sweet, which had been burnt to the point that it was almost rock like. "It's fine… The frosting really makes… Makes up for it…" Shadow said with a weak smile. Maria smiled and took a bite from hers. "Oh, I guess I might have burnt them more than a bit…" She said looking upset. "Don't worry. You'll get better with practice… I'm sure Shadow likes them. Don't you Shadow?" Professor Gerald asked, startling the duo. "Grandpa! Don't scare us like that." Maria said laughing. "I can't help it… It seems the older I get the quieter I move." Professor Gerald said. He then looked at Shadow and asked "Well? Do you like it?" Shadow nodded and swallowed, not matter how hard his stomach told him not to. Shadow smiled and said "It was great. Next time you'll have to make one for the Professor." The three of began to chatter and move on in several conversations.<p>

* * *

><p>Shadow noticed Tails standing next to him, Tails was surveying the various sweets and treats. "You enjoying the party?" Shadow asked, not getting a response from the fox. "Tails?" Shadow asked noticing that he had frozen in place. Shadow looked around the party and saw that everything had been stopped. Pinkie was in the middle of a jump and was floating inches off the ground. "Hey Shadow." Sonic's voice was suddenly behind him. Shadow whirled around and saw Sonic standing there. "Sonic? What happened to you?" Shadow asked taking a step back from his blue friend. "The Infection happened to me. I just wanted to thank you." Sonic replied. "Thank me? For what?" Shadow was confused, this just didn't make any sense to him.<p>

"If it wasn't for your little spring this wouldn't have happened." Sonic explained. "My… Spring…?" Shadow asked, he felt the room spin and he was in the Corrupted Spring Chamber. Sonic pointed upwards and Shadow tilted his head to see what Sonic was pointing at. There were several bee hives on the roof of the cave. "Months of Rainbow Honey…" Sonic began, the hives each began to drip different colored honey drops. Red, orange, yellow, blue, green, and purple. "Mixed with one test subject…" Sonic continued, the scene changed once again. A rabbit was trying to drink from the spring but fell in the thick blood like liquid. It rose out zombie like. It tried to attack a Manticore but it was able to escape unharmed. "Gave birth to the Infection." Sonic finished. Shadow felt his heart stop.

Even unknowingly he had once again caused the possible deaths of thousands. He turned to face Sonic who took on a softer expression. "Don't look so upset, after all… We could really use you. What do you say? Partners?" Sonic asked reaching out a hand. Shadow slapped it away and said "You were a hero once… Now you've become the very thing you used to fight." Sonic looked confused and asked "I've become Eggman?" Shadow looked angry and replied "NO! A villain!" Sonic smiled and Shadow noticed a flashing. "Looks like Chaos Control is fading… Goodbye for now…" Sonic said. Shadow blinked and the party had resumed. Pinkie landed, and Tails noticed Shadow. "Shadow…? You all right? You looked like you've seen a ghost…" Tails noted. Shadow looked around the room and said "I need to speak with you privately." Shadow grabbed Tails by the arm and began to lead him through the crowd. They exited the barn and moved towards the deep orchard. "What is it?" Tails asked. "I know what caused the Infection…" Tails went wide-eyed at the information given.

"You do? What did?" Tails asked. "I… I did… I didn't even mean to. It was this spring I had used when I led the changelings… It was mutated by magical honey or something I'm not sure…" Shadow explained. Tails was in utter shock, he wasn't sure how he should feel. "I… I can understand if you hate me." Shadow added. "Shadow. I could never hate you. You're one of my friends… I cannot, I repeat cannot, hate any of my friends." Tails said with a smile. Shadow nodded before the two rejoined the party.

* * *

><p>Flare moved through the forest, he leapt over the fallen tree in his path and continued forward. He held the yellow Chaos Emerald in his right hand, not letting go of it for anything. He looked back and didn't hear his pursuers anymore, so he began to slow his pace. He looked up and saw clear morning skies. He heard the chatter of animals ahead. He moved onwards and saw a small cottage ahead, there was a fenced off area with lots of animals filling it. He saw a familiar face and approached. Knuckles spread bird seed around for the birds and squirrels, he seemed to be at peace here. He looked over when he heard a twig snap. He saw an orange hedgehog with black shoes standing there. "Flare? Is that you? How's it going buddy?" Knuckles asked. Flare stepped forward and smiled. "Things have been going great. I'd heard about Fluttershy… I'm sorry…" Flare replied. His smile had turned into a frown. "I never thought this would happen… I mean…" Knuckles had begun, but stopped.<p>

"Knuckles, before I forget I got the yellow Chaos Emerald. Here." Flare handed the jewel to Knuckles who showed him inside. "You can stay as long as you'd like… If you don't mind doing some chores from time to time." Knuckles said with a large grin. "I don't. I think I should help out a bit anyway." Flare replied. Knuckles began to give Flare a task, while he went outside and continued feeding the animals.

* * *

><p>Well, I got another chapter up! This one comes with a special message! No longer on Hiatus, POKEMON MYSTERY DUNGEON GATES TO EQUSTRIA! I'm still looking for some Pokemon OCs. Please submit them via review on the story (OCs submitted on this story will NOT be accepted. You have been warned!), or Private Message me with the details. You'll need the name, Pokemon species, team name, four moves, and short backstory. Thank you! I also wanted to talk about this story, I believe it is going very well so far, but I want your opinion as well. Please give me anything that could improve the story. I really want to make this as good as I possibly can!<p>

I'm also throwing out some ideas for other crossovers and you can decide which one I do! Only Private Message votes will be accepted, I apologize if that inconveniences any of you, but it makes things simpler for me. These are the ideas:

Battle of the Dragons (MLP/Multi-Crossover)

Spike and the Mane Six find themselves in a different world, where dragons, good and evil battle for dominance over the beautiful place. Some dragons include: Paarthurnax (Skyrim), Valoo (LOZ Wind Waker), Spyro (Spyro series), Ridley (Metroid), Bull (Nickname for the single male dragon from movie _Reign of Fire_), and Toothless (How to Train Your Dragon).

Ben 10: Ridley's Chaos (Ben 10/Metroid Crossover)

Ben, Rook, Gwen, and Kevin have to face the biggest threat ever, blood thirsty pirates led by a giant Space Dragon. However, they will not face this threat alone, for the Hunter is on their side.

Shadow and Samus: Heroes of the Galaxy (Sonic the Hedgehog/Metroid Crossover)

Shadow and Samus team up to defend earth from both a resurrected Black Doom, and a vengeful Ridley. Who will win?

Fluttershy's Dusk (MLP/Pokemon Crossover)

While investigating a mysterious report of ghosts, Fluttershy bonds with a Pokemon none would have expected her to like. Join Fluttershy and her Pokemon on a journey to prove she can be a strong Pokemon Trainer.

So tell me what you think and if I get nothing then I'll randomly choose one of them… Please leave me a vote and remember! Private Message only! Thank you!


	5. Chapter 4

Chapter 4: Goodbye Ponyville Hello Robot

Shadow sat in the library and watched as Tails mixed together a few chemicals. "So why do you need me here?" Shadow asked. "Star Mane is coming over and I need you to entertain her while I work. I lost three weeks of work because of Pinkie…" Tails said, Shadow noticed the bags under his eyes and let out a sigh. "How long has it been since you slept?" Shadow asked, he was getting worried because Tails would often wobble and nearly fall. "I've been up for seven weeks straight…" Tails replied. Shadow's jaw dropped, he had been up for seven weeks without sleep. "How have you not crashed yet?" Shadow asked, he was amazed. "Coffee… Lots and lots of coffee…" Tails began to wobble again and Shadow caught him as he fell. "Thenk you…" Tails said, Shadow began to drag Tails towards a couch and said "You need to sleep." Tails began to flail his arms wildly shouting "NO! I CAN'T SLEEP! I NEED TO FIND A CURE!" Tails turned and slapped Shadow, which woke the fox up. Tails began to back away and said "It was an accident! I didn't mean to do it!" Shadow glared at Tails before shouting "YOU'RE DEAD FUCKER!" Tails ran out from the library screaming in terror.

Star Mane watched as Tails ran past her screaming, which made no sense. Why would he be screaming? She looked and saw a pissed off Shadow pursuing him, then everything made sense. "I'd better go get Twilight…" Shadow chased after Tails, he kept moving at a steady pace, not too fast, not too slow. Tails would tire out eventually, and Shadow would be ready.

"HELP! HELP ME!" Tails shouted running through the town, ponies looked out of windows in confusion, and many came out see what was going on. Shadow kept following while Tails ran for his life. "YOU'RE DEEEEAAAAD!" Shadow taunted from behind the fox. Eventually Tails found himself at a dead end, he pressed his hands on the wall and looked back to see Shadow standing there. Rainbow Dash, Twilight, and Speedy managed to find the duo and flew in to stop it. Shadow walked forward and slapped Tails across the face. "There. We're even now." Shadow said reaching out a hand. Tails took it and got onto his feet. "Now go back to the library and sleep." Shadow ordered. "I can't! I need to find a cure!" Tails shouted. "You need to sleep Tails, how can you find a cure if you collapse?" Shadow asked attempting to remain calm. "I guess you have a point… I… I'll go get some sleep…" Tails replied nervously.

Shadow nodded as Rainbow Dash slowed down and stopped. "You chased him through town just for a little slap?" Rainbow Dash asked. "To knock some sense into him." Shadow responded, he turned and began to walk towards the library. He entered to see Tails curled up on the couch, just as Star Mane knocked on the door. Shadow opened it and asked "Can I help you?" Star Mane smiled and replied "I'm here to speak with Tails." "He's asleep right now, come back later." Shadow said attempting to close the door gently. Star Mane stopped it with her hoof and said "It's very urgent, I really need to speak with him." "You just want to talk with him about our planet and the different beings we've encountered." Shadow said, going to shut the door again, but Star Mane stopped it. "I really need to speak with him…" She had begun but Shadow cut her off. "How about you talk with me? I can tell you a lot about some aliens…" Shadow suggested. "I suppose that would suffice." Star Mane replied, before Shadow exited the library and leaned on the trunk of the tree.

"What do you want to know?" Shadow asked. "Last time we spoke you'd mentioned an alien known as Black Doom. Could you tell me more about him?" Star Mane asked. "Black Doom was the leader of an alien race known as the Black Arms. The Black Arms were a violent race, easy to pick out from their black and crimson coloration, much like myself. Black Doom had helped in my creation, but swore he would return to Earth and destroy the planet. However, he required the seven Chaos Emeralds in order to do it. So he sought me out to collect them for him. I had believed him and gathered all seven Emeralds but he betrayed me, so I killed him and destroyed the Black Comet that the aliens knew as home…"  
>Star Mane was impressed by all this information, alien beings with malicious intent.<p>

"Not all aliens are evil though… Sonic and Tails had encountered a few of them… He had called them… Wisps… I believe… They were able to fuse with Sonic temporarily in order to share their power with him. The Doctor was using them to create a mind control device… Sonic was able to foil the Doctor's plans however…" Shadow explained. "So they were good aliens?" Star Mane asked. "Yes." Shadow replied. Shadow looked over at the Pegasus and asked "Anything else?" She shook her head before walking off happily. Shadow went into the library and saw Tails working. "Go back to sleep!" Shadow shouted, while the fox set down the chemicals and ran back towards the couch before leaping onto it.

Shadow sighed and began to leave the library, he had been requested by Pinkie and he didn't have anything to do for the rest of the day. He closed the door behind him and moved towards where Pinkie had told him to meet her. Tails opened his eyes and tiptoed over to the large collection of chemicals and began to work once more. As tired as he was he just couldn't stop working, no matter what anyone said.

Tails began to pour chemicals gently into a larger beaker. "Just a little more…" He muttered until the chemical finished pouring. His stomach growled, but he did his best to ignore it. "All right… Now I need some…" He reached for a beaker but found that it was just out of reach, he kept wiggling his fingers in an attempt to grab the glass, but he couldn't, not once did he look towards where he was reaching. "Come on… Stupid thing…" Tails muttered. He felt it get pushed into his fingers, making him smile. "Thank you." He said. "You're welcome." Fluttershy replied, Tails froze when he heard the voice. He did what his instincts told him to do… "AAAAAAAAAAHHHHHHH!" Tails ran out from the library and towards Sugar Cube Corner.

Shadow sat next to Pinkie who had prepared a dozen cupcakes. "Now we frost them!" Pinkie shouted with a giant smile. Shadow picked up a frosting bag and began to squeeze it, making the sweet substance come out from the end and onto the cake. He let out sigh of boredom and continued frosting the cupcakes, he didn't have anything better to do… Shadow's right ear twitched as he heard a yell. Tails flung the door open, locked it after entering and ran over to the black hedgehog. "SHADOW! FLUTTERSHY! LIBRARY! SCARED! INFECTED! Oh, cupcakes!" Tails shouted getting distracted by his stomach. "What…?" Shadow asked confused until he saw Fluttershy standing outside the door, she waved a hoof before tapping on the window and pointing at the lock.

Shadow began to reach for a knife on the counter, a large one most likely used for cutting cakes, but he felt a hand hold down his wrist. "I wouldn't do that if I were you." Scourge said with a large grin. Shadow watched them, their fangs had become shorter, maybe filed down… Scourge picked up the knife and moved over to the door, he flipped the lock and allowed Fluttershy to enter. "I'm sorry… I just want you to feel as good as we do… I mean… If you want to… We won't force you… Will we…?" Fluttershy began to ramble, she looked at Scourge who said "We will force you if we have to." His smile had become a frown. He watched as Shadow reached under the counter for something. "Yeah… Don't worry… There's nothing you have to worry about…" He revealed a flask and began to pour a yellowish liquid into his mouth. "Something to calm your nerves?" Scourge asked, Shadow shook his head, his cheeks were full of what Scourge assumed was alcohol and he hadn't swallowed yet. He revealed a lighter and in one quick moment he activated it. "What you gonna smoke too?" Scourge asked again, Fluttershy began to back up. Shadow spit the liquid out in a stream, creating a string of fire in front of him. Fluttershy let out a cry of fear and ran outside the building, while Scourge took the flames. He yelled in shock as he was engulfed in flames.

"What was that Shadow!?" Tails demanded to know, he wasn't sure if having any form of liquor was smart. "Remember your failed attempt at the cure?" Shadow asked, while Tails began to think. "You mean the…?" Tails began but Shadow cut him off. "Lighter fluid you accidentally created. I thought it might come in handy." Shadow tossed the empty flask behind him and got up. "We better find the others." He said before leading the group outside, Scourge stood there with several burn marks across his body.

"Really? You'll have to try harder than…" Scourge began but was cut off when a metal fist made contact with his jaw knocking it off his skull. Omega lifted Scourge by his head and threw him through the window shattering the glass. Fluttershy let out an "Eep!" and began to run away from the large robot. Omega turned to face Shadow and reached out a hand. "Tails, since we don't have Rouge with us… You are now a temporary member of Team Dark. You're our wings… Er… Flight, I'm the speed, and Omega is the strength. Got it all?" Shadow asked, getting a nod from the little fox. "Good. Let's go!" Shadow ordered running out from the building with Omega, Tails, and Pinkie following.

"Shadow we need to get to the library! I have some armor there! We can probably fit Omega and Gamma with some of it as well!" Tails shouted, avoiding a bite from an infected pony. "Look out!" Tails shouted, shoving the black hedgehog away from the pony as it chose a new target. Tails spun and smacked the stallion several times in the face with his tails, stunning the pony. Shadow pulled a small bottle from his bag and uncorked it. He threw the contents at one of them and the infected began to melt into a strange gray liquid. "What was that?" Tails asked astounded. "Cockatrice blood, melts the fuckers… Not sure why though…" Shadow replied, while Omega dealt with a few infected.

"C'mon guys! You need to chill out! We just want to help!" Sonic shouted at them, while the group turned to face the hedgehog. "You really think this is going to end well? I'm not afraid to fight you!" Shadow shouted, he watched as Sonic laughed. "You seem to have forgotten, I'm basically invincible! You can't kill me, or beat me!" Sonic replied, he ran at Shadow, who rushed forward. The two hedgehogs moved close to each other, Sonic attempted to punch Shadow, but Shadow was able to dodge the attack made. Shadow kicked Sonic in the chest, knocking him a few feet away. However Sonic rose onto his feet and moved, Shadow tried to dodge a kick, but felt Sonic's foot make contact with his forehead. Shadow was flung several feet back, but he landed perfectly. The two hedgehogs charged at each other again and began fighting, it was a flurry of fists and feet as they fought.

Omega however had been angered, he grabbed Sonic by the waist and hoisted the hedgehog into the air. "Hey! W-Wait a minute big guy! Don't you dare…" Sonic began but it turned into a scream as Omega threw Sonic with all his might into the sky. Omega turned and nodded, while they ran for the tree house. Zecora, Twilight, Rainbow Dash, Applejack, Big McIntosh, Speedy, Rarity, Scootaloo, Sweetie Belle, Star Mane, Gizmo, Flare, Knuckles, Gamma, Metal Sonic and Spike were inside. "There you guys are!" Knuckles shouted, he looked at them and said "Suit up, we're leaving town." Shadow placed some of the armor, it wasn't heavy so he wasn't sure about it. Tails began to cork some beakers and test tubes, making sure they were ready for travel. "Can't lose my research, like last time." Tails said giving Pinkie a quick glare.

"What do you mean?" Rarity asked, not having heard of the incident. "Oh, don't worry about it Rarity, we have to go… Besides, we wouldn't want to bore the readers with something they've already read in the last chapter." Pinkie said with a big smile. Tails leaned over to Twilight and asked "What is she talking about?" Twilight shrugged and replied with "Don't question Pinkie. Something I learned fairly fast." Twilight explained with a roll of her eyes. There was a pounding on the door, the infected could be heard as they slammed on the wooden barrier between them and the uninfected. Shadow looked at the group and asked "Where are we going?" All he received were uneasy glances. "We haven't really figured that much out yet… What we do know is that it has to be far away from here!" Twilight replied, after about two minutes. "What help is that?" Shadow asked, trying to keep calm. "We just need to find a way to get out of here first…" Tails said nervously.

Shadow nodded and faced the door, it would hold for a while, but then what? What if they found another way inside? Shadow groaned in frustration, he had no idea what to do. "Twilight. Is there a window upstairs?" Shadow asked. "Well… Yes, but I don't see how that…" Shadow ran up the stairs and towards the window. He opened it and looked down, there was nothing underneath it making this their only escape route. He ran back down and began to explain his plan. "We need to jump out the window in order to escape. I'll go first and I'll distract them from getting to you. Then you all run and get as far away from this town as possible!" Shadow said in a quiet voice. He led the group upstairs when he heard the door give in, there was a loud crash and the sound of fighting.

Shadow turned around and saw Big McIntosh was fighting them back with a chair, holding it in his teeth he swung it at them. He threw the chair and it made contact with one of the infected. "Go! Get out of here!" He shouted, while Shadow began usher ponies out the window, they all landed with thuds, but were unharmed. Shadow jumped out leaving Applejack and Big Mac still in the building. Applejack turned to face her brother, she said "Be careful…" Big Mac smiled and replied with "Eeyup." Applejack jumped and landed on her hooves. She saw the group had already begun to move, so she ran to catch up.

There was a loud yell as the infected noticed them, rushing at her Applejack had to move quickly. She saw them closing in on her, but Shadow kicked one in the face. He watched as they began to back away from him while he held the headless cockatrice. "Make a move… I dare you." Shadow said narrowing his eyes. Shadow watched as they backed away, leaving a large gap for Applejack to get through. She ran past by the others while Shadow turned and moved over to the group. He dropped the headless cockatrice onto the ground and began to walk away while the rest of the group followed in silence.

* * *

><p>Shadow sat under the large tree, it blocked the sun from hitting him and he needed it. The middle of summer in a sunny field, he watched as Sweetie Belle and Scootaloo ran around the flowers, with Twilight and the others not far from them. He wasn't sure why but it seemed like the two fillies were always watching him, he'd catch them glancing at him from time to time, it was usually when he was doing something. He thought back to just earlier today…<p>

* * *

><p>Shadow had been searching for a way to get a look at their surroundings, if they didn't know where they were it would end up a disaster. He placed his hand on the trunk of a sturdy tree and looked to his left. There was a second tree, about the same size and width. They were close enough that he could get his way up to the top. Shadow jumped, pressing all of his weight onto the tree, he then used it to launch at the second tree, once again pressing all his weight into it, and he sprung back and forth between the trees rising with each jump. He grabbed the top of the tree and began to search for anything that could provide some form of cover. He saw a field, it had many flowers, some trees that seemed like there was fruit in them, a few streams, and finally what appeared to be several bushes. He looked down and jumped, grinding on each tree branch until he felt his feet hit the ground. Sweetie Belle and Scootaloo looked at him in awe, to them he was the very definition of "fearless". Shadow had begun to explain where they were going but the two didn't listen. They were instead telling each other how amazing he was.<p>

* * *

><p>Shadow chuckled as he came back to reality, he noticed Scootaloo was doing something, she continuously jumped up and down on a spot in the field. Shadow could hear a muffled metallic clunk as her hooves hit the ground. Shadow walked over, attracting the rest of the group as well. He yanked at the ground and pulled away a blanket woven from grass. It was actual grass, whoever made this didn't cut any corners. He turned his attention to the hatch that he had revealed, wasting no time he grabbed the handle and opened the metal door. "I'm going to investigate this… Don't follow me." Shadow said, but he mostly looked at the two fillies, who both gave sad faces.<p>

Shadow jumped into the long round corridor, his shoes hitting metal as he landed. Shadow began to walk down the pathway made, fully aware for anything that may be dangerous. He listened for any sign of danger, not wanting to get ambushed by anything. He stopped moving when a loud crash was heard before him. He continued moving forward, but at a slower pace. Then in a quick motion he was knocked onto his back. The robot looked at him, it was clearly broken, cracks covered its head, many wires were torn apart, and its left eye wasn't lighting up. Upon closer inspection Shadow noticed that it seemed to be the skeleton of a robot.

"Hello… You seem to be lost… I'm afraid I have to kill you now…" It said in a sweet, gentle tone. _"Shit…" _ Shadow thought as he recognized the voice. It was Metal Fluttershy, somehow she had survived him destroying the factory, and it seemed to have damaged her beyond being able to fully repair herself. Shadow kicked her off and ran back towards the exit, only to find himself at a different door. He flung it open and slammed it shut behind him. Turning he found himself face to face with another robotic skeleton. "GAH!" Shadow let out a cry of surprise.

He noticed the skeleton didn't make a move for him so he tapped it on the nose. It fell to the ground, not having any power. He looked around the room closer, and saw it filled with various skeletons of machines. Each one from the robots that were thought to be destroyed when the factory exploded. Many of them had parts missing, most likely scavenged by each other when they eventually shut down. It seemed that Metal Fluttershy was the only survivor left. He looked at the tools on the ground, and noticed that one robot however was still fully intact, and if any damage had been done it wasn't visible. The Shadow Android sat against the wall, it appeared just as it had when he fought it in the factory.

A scraping sound got his attention, it seemed to be coming from inside the walls, and it traveled until it went into the ceiling, towards a vent cover. Shadow turned and attempted to open the door, but it was stuck. "Come on come on come on!" He began to slam into the door, attempting to break it down. "Open! God dammit!" Shadow shouted continuing to slam himself into the metal door. Metal Fluttershy broke the vent cover and dropped into the room. She moved towards Shadow, who was still trying to break down the door. Shadow couldn't take her on, not down here. He could barely see so he had a large disadvantage. Metal Fluttershy was nearly to him, ready to fight. The moment Shadow was able to see her, a lead pipe made contact with her head, knocking the robot away and shutting it down. Shadow saw Tails approach and smiled. Tails managed to pick the lock to the door, and Shadow left, leaving Tails down there alone. He searched for anything useful and found only a few tools, a screwdriver, a hammer, and a few pieces of metal.

About halfway through the door, Tails felt a metal hand wrap around his ankle. He let out a cry of shock as Metal Fluttershy pulled him onto the ground, the objects he had picked up falling around him. Tails clawed at the metal floor trying to get away from the robotic monster. "You're doomed…!" She said lifting up one of her arms, the metal on the hoof was jagged and broken giving it a knife like form. She quickly swiped Tails across the back of his leg and pulled him down further. She slashed his back, leaving a large gash. She pulled him down even further and focused at his head. _"This is it… I'm going to die… I'm sorry Sonic…" _He thought, he looked back at Metal Fluttershy who had her weapon raised, ready to strike. Shadow kicked her skull, causing her to release Tails. Tails scrambled onto his feet and towards the exit leaving a trail of blood as he moved. Shadow followed and climbed back to the surface.

"What happened!?" Twilight asked, seeing the bleeding fox and the bruised hedgehog. "One of Eggman's robots. Metal Fluttershy managed to survive the explosion, they all did. As they shut down, they used each other as spare parts. Now, none remain." Shadow explained, while he closed the hatch. Written in fading paint was "Failed Experiments. Do Not Enter!" Shadow groaned and moved back over to the tree where he sat down once again. He was approached by Sweetie Belle and Scootaloo who were carrying a basket of apples, picked freshly from the trees. He took and bit into one, feeling the juice run down his throat, he swallowed and looked around the area, and this place was nice, not perfect, but nice. Shadow smiled and drifted to sleep in their little Eden.

* * *

><p>"Shadow? Have you ever wondered why Grandfather works all the time?" Maria asked the black hedgehog. "The Professor say's his work will help those on Earth." Shadow replied. "It must be important… I barely see him anymore." Maria said with a frown. "The Professor said he was taking tomorrow off, so that he could spend more time with us." Shadow said, making Maria smile a bit. "He did?" She asked. Shadow nodded and looked out the ARK's window, he looked at the blue planet below and felt himself grow with wonders. Would he ever see it? What were the people there like? Would they accept him?<p>

Shadow felt a hand grab onto his shoulder, he faced the Professor who smiled warmly at the hedgehog. "Shadow… I need to talk with you… Alone." Shadow nodded and followed the Professor into a room where no one would be able to hear them. "I have recently come to terms with myself… Shadow… I won't be around forever… I need you to promise me something…" The Professor said, making the black hedgehog feel nervous. "Yes? What is it?" Shadow asked. "Promise me… No matter what… You'll take care of Maria… You and I… Are the only family she has left…" Shadow was shocked, but he knew what he had to do. "I will Professor. I'll protect her with every part of my power." Shadow replied. The Professor smiled and left the room leaving Shadow alone in the darkness.

* * *

><p>Shadow awoke to a loud pounding, he looked and saw the metal hatch throb with each hit. "Let… Me… OUT!" Metal Fluttershy screamed in rage. Sweetie and Scootaloo backed up frightened, but Shadow stood in front of the hatch making sure it would hold. He stomped on the metal and heard her shout "I'LL RIP YOUR EYES FROM THEIR SOCKETS! I'LL TEAR YOUR FUCKING ENTRAILS FROM YOUR GUT! I'LL FEED YOUR CORPSES TO THE MANTICORES AND WHEN THEY'RE DONE WITH YOU YOU'LL ALL BE NOTHING MORE THAN LITERAL PILES OF SHIT!" She began to laugh, while pounding on the hatch. "The only piece of shit is you! Make sure to tell your robotic buddies that they're nothing but fucking shit just like you!" Shadow yelled, which made her stop.<p>

"I'll come down there and I'll finish you off! I'll use your Goddamn head like a trophy! If you didn't think that was enough, then I'll use your wires to strangle each and every cockatrice I see! Then… Oh ho the… I'll use your hooves as chair fucking chair legs!" Shadow shouted, he heard footsteps moving away from the hatch quickly, making him smile. "She won't be bothering us again." Shadow said to the group who stood wide eyed at him. Rarity had covered Sweetie Belle's ears, while Rainbow Dash did the same with Scootaloo. "You've gotta do what you've gotta do." Shadow said before moving away from the hatch, he moved over to his tree and leaned on it. Shadow placed a cigar in his mouth and lit a match, he stared at it for a bit before waving it out and placing the cigar back in his bag. He didn't want to do this too often, after all he did have small children with him. "Twilight. Are you sure it was a good idea to bring him along? He doesn't seem to be very… Preferable as a leader…" Rarity began, but Applejack bumped into her in an attempt to stop her before Shadow could hear.

"It ain't smart to be talkin bout that feller when he can probably hear yah." Applejack whispered. "I understand Rarity, but he's fought Sonic before. He may know how to beat him." Twilight said in a hushed voice. "He's a brute!" Rarity hissed, pressing her head against Twilight's. "He's our only hope!" Twilight whispered back. "He's going to lead us into certain doom!" "He's going to help us out!" "He has horrible fashion sense!" "He has what it takes to survive!" The two mares glared at each other until Shadow said "You do know you're only about three feet away from me? I heard everything."

* * *

><p>Scourge was trying to place his jaw back onto his skull, it finally cracked into place and he lifted his fists in triumph. He heard a screaming as Sonic landed nearby the green hedgehog. "You didn't stop him did you?" Scourge asked. "Yes, I always plummet from at least fifty feet because I stopped them from escaping…" Sonic replied in a sarcastic tone. "Why does this always happen to me…?" Sonic asked, getting onto his feet. "What?" Scourge asked curiously. "There seems to be a pattern of me falling onto my face… After Tails and I first attacked the Egg Carrier… When I had first been turned into a Werehog… After Merlina summoned me to Camelot…" Sonic explained, he knew this had to just be some form of cruel joke. "Sonic, we've captured one." Trixie announced moving over to the two hedgehogs.<p>

Big McIntosh was being herded by the infected, he had several bruises and cuts but no bites. "So… You were trying to escape with the others correct?" Sonic asked. "Eeyup." He replied, his face was void of emotion, so Sonic couldn't tell if he was afraid or not. "You going to tell me where they're heading?" Sonic asked. "Nope." Big Mac answered. Sonic scowled and snapped his fingers, the infected knocked Big Mac's feet out from under him. The infected began to kick him, making him cough up blood. Sonic bent down and asked "You gonna tell me now?" Big Mac spit in his face, Sonic wiped away the mixture of blood and saliva before kicking Big Mac in his jaw. "Tell me now!" Sonic shouted. "Nope. Ah can't." Big Mac muttered between gritted teeth. "Why not!?" Sonic asked now furious. "Ah'd have ta know where they're goin first…" Big Mac replied. For some reason he smiled when Sonic began backing away in shock. "No… No…! NO NO NO NO NO NO NO NO NO NO NO NO NO!" Sonic yelled. He grabbed his left ear and felt it come off in his hand. He tossed the ear aside and looked at Big Mac.

"You will not make a fool of me!" Sonic shouted. "Ah just did." Big Mac said with a grin. Sonic kicked him in the stomach "You son of a bitch!" He shouted, but he continued to kick, soon Big Mac began to bleed, Sonic's shoes had broken through the skin, allowing the red liquid to flow freely. Sonic kept kicking, he only stopped when Silver and Scourge forced him to stop. "We could use him Sonic, let's just infect him and get it over with!" Scourge said. Sonic nodded as the infected surrounded Big Mac, his red coat was unable to be seen through the wriggling mass of the infected fighting over trying who got to infect the large red stallion.


End file.
